Contacts of the helix formed by residues 384 - 392 (chain F) in PDB entry 5ZRV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 384 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231F ALA* 5.3 10.3 - - - -
241F GLN* 4.5 17.6 + - - -
382F PHE 3.6 0.8 + - - -
383F SER* 1.3 71.1 - - - +
385F GLN* 1.3 52.0 + - - +
386F ILE 3.1 3.5 - - - +
387F LEU* 2.9 7.8 + - - +
388F ALA* 2.4 36.0 + - - -
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Residues in contact with GLN 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227F ALA 5.9 2.2 + - - -
230F LEU 6.3 0.9 - - - -
231F ALA* 5.5 5.6 - - - +
352F LEU 5.4 6.6 - - - +
382F PHE* 3.7 7.1 + - - +
383F SER 3.0 9.3 + - - -
384F GLY* 1.3 72.0 - - - +
386F ILE* 1.3 57.9 + - - +
388F ALA* 3.4 2.6 + - - +
389F ASN* 2.8 23.9 + - - -
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Residues in contact with ILE 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379F HIS 5.8 3.8 - - - -
380F GLU* 6.0 4.0 - - - +
382F PHE 3.9 9.8 + - - -
384F GLY 3.1 1.8 - - - +
385F GLN* 1.3 75.5 - - - +
387F LEU* 1.3 59.2 + - - +
389F ASN* 3.2 5.8 - - - +
390F PHE* 2.9 17.3 + - - -
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Residues in contact with LEU 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384F GLY* 2.9 12.8 + - - +
386F ILE* 1.3 75.4 - - - +
388F ALA* 1.3 55.1 + - - +
389F ASN 3.2 0.4 - - - -
390F PHE* 3.0 4.6 + - - +
391F LYS* 2.6 31.2 + - - -
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Residues in contact with ALA 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F LEU 5.5 6.5 - - - -
231F ALA* 6.2 1.6 - - - +
234F PHE* 5.7 8.5 - - - +
384F GLY 2.4 21.3 + - - -
385F GLN* 3.6 2.9 - - - +
387F LEU* 1.3 72.8 - - - +
389F ASN* 1.3 54.1 + - - +
390F PHE 3.1 1.1 - - - -
391F LYS* 4.0 2.2 - - - +
392F ALA* 3.1 26.5 + - - -
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Residues in contact with ASN 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356F THR* 6.0 4.4 - - - +
385F GLN 2.8 15.5 + - - -
386F ILE* 3.2 11.0 - - - +
387F LEU 3.2 0.2 - - - -
388F ALA* 1.3 73.2 - - - +
390F PHE* 1.3 56.3 + - - +
392F ALA 5.0 0.7 - - - -
393F MET 5.7 1.3 - - - -
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Residues in contact with PHE 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386F ILE 2.9 11.7 + - - -
387F LEU* 3.0 6.8 + - - +
389F ASN* 1.3 79.9 - - - +
391F LYS* 1.3 62.8 + - - +
392F ALA 3.5 0.7 - - - -
393F MET 4.1 1.6 + - - -
394F ASP* 3.6 16.6 + - - -
410F GLY 5.4 0.5 - - - +
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Residues in contact with LYS 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234F PHE 5.7 5.4 - - - -
387F LEU 2.6 19.5 + - - -
388F ALA* 3.3 2.8 + - - +
390F PHE* 1.3 73.5 - - - +
392F ALA* 1.3 63.1 + - - +
393F MET 3.4 0.7 + - - -
394F ASP* 3.5 11.3 + - - +
395F SER* 4.1 3.3 + - - -
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Residues in contact with ALA 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388F ALA* 3.1 15.5 + - - +
390F PHE 3.5 0.2 - - - -
391F LYS* 1.3 78.4 - - - +
393F MET* 1.3 56.9 + - - +
395F SER* 3.5 18.0 + - - +
396F ASP 4.2 5.7 - - - +
398F PHE* 5.3 5.4 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il